aTyr Pharma, Inc. (NASDAQ:LIFE) Q4 2022 Earnings Conference Call March 9, 2023 5:00 PM ET Company Participants Ashlee Dunston - Director, Investor Relations & Corporate Communications Sanjay Shukla - President & Chief Executive Officer Jill Broadfoot - Chief Financial Officer Conference Call Participants Gregory Renza - RBC Capital Markets Sara Nik - H.C. Wainwright Yale Jen - Laidlaw Operator Good afternoon, ladies and gentlemen, and welcome to the aTyr Pharma Fourth Quarter and Full Year 2022 Conference C ...

Financial Position - The company reported an accumulated deficit of $410.1 million as of September 30, 2022, compared to $372.3 million as of December 31, 2021[87]. - Cash, cash equivalents, restricted cash, and available-for-sale investments totaled $79.6 million as of September 30, 2022, down from $107.9 million as of December 31, 2021[87]. - As of September 30, 2022, the company has material cash requirements primarily related to its operating lease and financing lease agreements, totaling significant ongoing obligations[102]. - The company anticipates financing its cash needs through equity offerings, grant funding, collaborations, and strategic partnerships, with potential dilution of existing stockholder interests[101]. Research and Development - The company initiated a global pivotal Phase 3 clinical trial (EFZO-FIT™ study) for efzofitimod, aiming to enroll 264 subjects with pulmonary sarcoidosis[76]. - Efzofitimod received orphan drug designation from the FDA for the treatment of sarcoidosis and systemic sclerosis, and fast track designation for pulmonary sarcoidosis[73]. - The Phase 1b/2a clinical trial for efzofitimod showed positive results in 37 patients, demonstrating consistent dose response on key efficacy endpoints[74]. - The company has focused resources on the efzofitimod program, delaying the initiation of a Phase 1 study for ATYR2810 due to current market conditions[81]. - The company has been advancing its discovery pipeline of tRNA synthetases and NRP2 antibodies, with new programs announced in February 2021[79]. - Research and development expenses increased to $9.9 million for the three months ended September 30, 2022, up from $5.1 million in the same period in 2021, representing a $4.7 million increase[118]. - For the nine months ended September 30, 2022, research and development expenses were $27.9 million, compared to $17.3 million in 2021, reflecting a $10.6 million increase[121]. - The increase in research and development expenses was primarily due to $3.0 million in start-up costs for the EFZO-FIT™ study and increased manufacturing costs[118]. - The company anticipates that research and development expenses will continue to rise in future years, focusing on clinical development and manufacturing of efzofitimod[111]. - The ongoing COVID-19 pandemic has caused delays in clinical trials, impacting the timelines and costs of product candidates[112]. - The company is unable to estimate with certainty the costs and timelines for future clinical trials due to the unpredictable nature of development[114]. Collaboration and Funding - The company entered into a collaboration with Kyorin Pharmaceutical for the development and commercialization of efzofitimod in Japan, with potential milestone payments of up to $165 million[77]. - The company received an upfront payment of $8.0 million and a milestone payment of $2.0 million under the Kyorin Agreement, with potential additional payments of up to $165.0 million based on future milestones[94]. - The company completed a public offering in September 2021, raising approximately $80.6 million from the sale of 10,781,250 shares at $8.00 per share[89]. - The company entered into an "at-the-market" offering program allowing the sale of up to $65.0 million in common stock, generating approximately $3.1 million in net proceeds from 951,175 shares sold at a weighted-average price of $3.55 per share during the nine months ended September 30, 2022[91]. - Under a previous offering program, the company sold 986,267 shares at a weighted-average price of $4.75 per share, resulting in net proceeds of $4.4 million in 2021[92]. - The company has a common stock purchase agreement with Aspire Capital, allowing for the sale of up to $20.0 million in shares, with $4.8 million remaining available for issuance as of September 30, 2022[93]. Operating Performance - For the nine months ended September 30, 2022, net cash used in operating activities was $(31.5) million, an increase from $(25.0) million in the same period of 2021, primarily due to increased R&D expenditures[96]. - Net cash provided by investing activities was $45.2 million for the nine months ended September 30, 2022, compared to $(42.2) million in 2021, reflecting timing differences in investment transactions[97]. - Financing activities generated $4.6 million in net proceeds from stock issuance during the nine months ended September 30, 2022, significantly lower than $80.6 million in the same period of 2021[98]. - The company has not generated any revenues from product sales to date and expects expenses to increase as it advances clinical development and seeks marketing approval for product candidates[99]. General and Administrative Expenses - General and administrative expenses for the three months ended September 30, 2022, were $3.6 million, an increase of $1.0 million from $2.6 million in 2021[119]. - General and administrative expenses for the nine months ended September 30, 2022, totaled $10.6 million, up from $8.1 million in 2021, marking a $2.5 million increase[122]. - Other income for the three months ended September 30, 2022, was $0.2 million, compared to $59,000 in 2021, indicating an increase of $188,000[120]. - Other income for the nine months ended September 30, 2022, was $0.6 million, up from $0.2 million in 2021, representing a $0.5 million increase[123]. Market Conditions - The ongoing COVID-19 pandemic and geopolitical tensions have introduced significant uncertainties affecting the company's operations and financial performance[86].

aTyr Pharma, Inc. (NASDAQ:LIFE) Q3 2022 Earnings Conference Call November 10, 2022 5:00 PM ET Company Participants Ashlee Dunston - Director, IR & Corporate Communications Sanjay Shukla - President & CEO Jill Broadfoot - CFO Conference Call Participants Joe Pantginis - H.C. Wainwright Hartaj Singh - Oppenheimer Edward Tenthoff - Piper Sandler Yale Jen - Laidlaw & Co Sean Kim - Jones Trading Kumaraguru Raja - ROTH Capital Partners Operator Good afternoon, ladies and gentlemen and welcome to aTyr Pharma’s Thi ...

Financial Data and Key Metrics Changes - The company ended Q2 2022 with $89.3 million in cash, restricted cash, cash equivalents, and investments [46] - Research and development expenses were $9.1 million for Q2 2022, which included costs for efzofitimod and 2810 programs, as well as start-up costs for the Phase 3 EFZO-FIT study [46] - General and administrative expenses were $3.4 million for Q2 2022 [46] Business Line Data and Key Metrics Changes - The company is advancing its Phase 3 study of efzofitimod in patients with pulmonary sarcoidosis, which is projected to be the largest interventional study for this condition to date [9][10] - The EFZO-FIT study is a global pivotal Phase 3 randomized, double-blind, placebo-controlled study to evaluate the efficacy and safety of efzofitimod [25] Market Data and Key Metrics Changes - The estimated patient population for pulmonary sarcoidosis is close to 200,000 in the US, 150,000 in major European markets, and 20,000 in Japan, with up to 75% requiring treatment [16][20] - The potential market opportunity for efzofitimod in sarcoidosis and other interstitial lung diseases is estimated to be between $2 billion to $3 billion in peak sales [23] Company Strategy and Development Direction - The company aims to position efzofitimod as a first disease-modifying therapy for pulmonary sarcoidosis, focusing on steroid reduction and improving patient quality of life [32] - The company is also exploring additional indications for efzofitimod in other forms of interstitial lung disease, where immunomodulatory treatment is the current standard of care [22] Management's Comments on Operating Environment and Future Outlook - Management expressed confidence in the regulatory alignment regarding steroid sparing as a primary endpoint, noting productive interactions with regulatory authorities in the US, EU, and Japan [56][58] - The management highlighted the excitement from the patient and provider community regarding the trial, which is expected to facilitate faster enrollment [61] Other Important Information - The FDA granted Fast Track designation for efzofitimod, which facilitates development and review for serious diseases with unmet medical needs [21] - The company has built an intellectual property estate of over 200 issued patents related to its tRNA synthetase platform, which is expected to be a defining part of its future [40] Q&A Session Summary Question: What is the level of regulatory alignment in ex-US countries regarding steroid sparing as a primary endpoint? - Management indicated that regulatory interactions have been productive, with universal support for steroid reduction as an approvable endpoint [56][58] Question: What are the broader challenges and risks to the timeline for enrolling patients? - Management noted the importance of planning and mobilizing sites effectively, emphasizing the strong performance of their clinical operations team [60][61] Question: Can you describe the exclusion criteria for the efzofit study? - Management explained that HRCT is now the preferred imaging method to ensure patients have active inflammation and are not too fibrotic [68][70] Question: What is the initial communication strategy for the upcoming Phase 1 study of 2810? - Management stated that they will provide details on the clinical protocol and data release strategy as the study progresses [74][76] Question: How does the tapering strategy in the efzofit study impact enrollment? - Management believes that the tapering strategy will enhance enrollment by providing patients with the opportunity to reduce steroid use significantly [82][84] Question: What are the main differences in developing targeted therapies between oncology and inflammation? - Management highlighted that while the modalities differ, the understanding of inflammation and fibrosis plays a crucial role in both areas, facilitating interactions with regulators [88][90]

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 (Mark One) For the transition period from to Commission File Number: 001-37378 ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 ATYR PHARMA, INC. For the quarterly period ended June 30, 2022 (Exact name of registrant as specified in its charter) (State or other jurisdiction of incorporation or ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2021 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction of i ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2021 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction of inc ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE EXCHANGE ACT OF 1934 For the transition period from to ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction of incorporation or organization) 3545 John H ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-37378 Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller ...